1kir: Difference between revisions

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<StructureSection load='1kir' size='340' side='right'caption='[[1kir]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1kir' size='340' side='right'caption='[[1kir]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1kir]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Chick Chick] and [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KIR FirstGlance]. <br>
<table><tr><td colspan='2'>[[1kir]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KIR FirstGlance]. <br>
</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kir OCA], [https://pdbe.org/1kir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kir RCSB], [https://www.ebi.ac.uk/pdbsum/1kir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kir ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kir OCA], [https://pdbe.org/1kir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kir RCSB], [https://www.ebi.ac.uk/pdbsum/1kir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kir ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/LYSC_CHICK LYSC_CHICK]] Lysozymes have primarily a bacteriolytic function; those in tissues and body fluids are associated with the monocyte-macrophage system and enhance the activity of immunoagents. Has bacteriolytic activity against M.luteus.<ref>PMID:22044478</ref> 
[https://www.uniprot.org/uniprot/HVM44_MOUSE HVM44_MOUSE]  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kir ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kir ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Using site-directed mutagenesis, X-ray crystallography, and titration calorimetry, we have examined the structural and thermodynamic consequences of removing specific hydrogen bonds in an antigen-antibody interface. Crystal structures of three antibody FvD1.3 mutants, VLTyr50Ser (VLY50S), VHTyr32Ala (VHY32A), and VHTyr101Phe (VHY101F), bound to hen egg white lysozyme (HEL) have been determined at resolutions ranging from 1.85 to 2.10 A. In the wild-type (WT) FvD1.3-HEL complex, the hydroxyl groups of VLTyr50, VHTyr32, and VHTyr101 each form at least one hydrogen bond with the lysozyme antigen. Thermodynamic parameters for antibody-antigen association have been measured using isothermal titration calorimetry, giving equilibrium binding constants Kb (M-1) of 2.6 x 10(7) (VLY50S), 7.0 x 10(7) (VHY32A), and 4.0 x 10(6) (VHY101F). For the WT complex, Kb is 2.7 x 10(8) M-1; thus, the affinities of the mutant Fv fragments for HEL are 10-, 4-, and 70-fold lower than that of the original antibody, respectively. In all three cases entropy compensation results in an affinity loss that would otherwise be larger. Comparison of the three mutant crystal structures with the WT structure demonstrates that the removal of direct antigen-antibody hydrogen bonds results in minimal shifts in the positions of the remaining protein atoms. These observations show that this complex is considerably tolerant, both structurally and thermodynamically, to the truncation of antibody side chains that form hydrogen bonds with the antigen. Alterations in interface solvent structure for two of the mutant complexes (VLY50S and VHY32A) appear to compensate for the unfavorable enthalpy changes when protein-protein interactions are removed. These changes in solvent structure, along with the increased mobility of side chains near the mutation site, probably contribute to the observed entropy compensation. For the VHY101F complex, the nature of the large entropy compensation is not evident from a structural comparison of the WT and mutant complexes. Differences in the local structure and dynamics of the uncomplexed Fv molecules may account for the entropic discrepancy in this case.
Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme.,Fields BA, Goldbaum FA, Dall'Acqua W, Malchiodi EL, Cauerhff A, Schwarz FP, Ysern X, Poljak RJ, Mariuzza RA Biochemistry. 1996 Dec 3;35(48):15494-503. PMID:8952503<ref>PMID:8952503</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1kir" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
*[[Lysozyme 3D structures|Lysozyme 3D structures]]
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Chick]]
[[Category: Gallus gallus]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Lk3 transgenic mice]]
[[Category: Mus musculus]]
[[Category: Lysozyme]]
[[Category: Fields BA]]
[[Category: Fields, B A]]
[[Category: Mariuzza RA]]
[[Category: Mariuzza, R A]]
[[Category: Poljak RJ]]
[[Category: Poljak, R J]]
[[Category: Bacteriolytic enzyme]]
[[Category: Egg white]]
[[Category: Glycosidase]]
[[Category: Hydrolase]]
[[Category: Immunoglobulin v region]]

Revision as of 11:00, 3 April 2024

FV MUTANT Y(A 50)S (VL DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 COMPLEXED WITH HEN EGG WHITE LYSOZYMEFV MUTANT Y(A 50)S (VL DOMAIN) OF MOUSE MONOCLONAL ANTIBODY D1.3 COMPLEXED WITH HEN EGG WHITE LYSOZYME

Structural highlights

1kir is a 3 chain structure with sequence from Gallus gallus and Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HVM44_MOUSE

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1kir, resolution 2.00Å

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